Personal details
Current position
1 Nov. 2022 to Present
Postdoctoral Scholar at the University of Tennessee Health and Science Center (Memphis, USA).
Reporting to Prof. Erik Garrison.
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Heterologous recombination in the human pangenome ( Guarracino et al., 2023, Nature)
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Formation and propagation of human Robertsonian chromosomes ( de Lima*, Guarracino*, Koren et al., 2024, bioRxiv)
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Nanopore sequencing for studying recombination in yeast
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Development of a new whole-genome aligner ( wfmash)
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Pangenome graph sorting and layout ( Heumos*, Guarracino* et al., 2024, Bioinformatics)
Collaborations
1 Nov. 2023 to Present
Honorary contract holder at the Princess Máxima Center for Pediatric Oncology (Utrecht, Netherlands).
Reporting to Dr. Ruben van Boxtel and Prof. Pjotr Prins.
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Personalized pangenome references for improved cancer genomics
1 Nov. 2022 to Present
E-Visitor at the Human Technopole (Milan, Italy).
Reporting to Prof. Nicole Soranzo and Prof. Erik Garrison.
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Building pangenome graphs ( Garrison*, Guarracino* et al., 2024, Nature Methods) ( PGGB, smoothxg)
1 Nov. 2019 to Present
Italian Institute for Genomic Medicine (Candiolo, Italy) and the Candiolo Cancer Institute (Candiolo, Italy).
Reporting to Dr. Ilio Vitale.
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Spindle Assembly Checkpoint functionality in colon-rectal cancer stem cell
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Exploiting karyotypic aberrations and chromosomal instability in cancer stem cells for precision immunotherapy
Employment
1 Nov. 2021 to 31 Oct. 2022 (1 year)
Postdoctoral Associate at the Human Technopole (Milan, Italy).
Reporting to Prof. Nicole Soranzo and Prof. Erik Garrison.
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Unbiased pangenome graphs ( Garrison and Guarracino, 2022, Bioinformatics) ( seqwish)
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Optimized Dynamic Genome/Graph Implementation (Guarracino et al., 2022, Bioinformatics) ( ODGI)
4 Mar. 2013 to 31 Oct. 2018 (5 years, 7 months, 28 days)
Computer engineer for multiplatform firmware/software development, GISA (Salerno, Italy).
Reporting to Eng.
Gaetano Giordano.
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Firmware development in STMicroelectronics microcontrollers for high-efficiency embedded systems
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Firmware and library development in open-source hardware and software platforms (Arduino/Genuino)
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Development of multi-management software and desktop applications for embedded systems programming
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Mobile applications development for programming and the control of multi-service machines via Bluetooth
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Implementation of proprietary communication protocols and contact/contactless (RFID) interfaces
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Development and maintenance of websites and an e-commerce
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Remote assistance to customers for the usage and programming of multi-service machines
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Patent application on a universal system for services fruition (ITUA20165252, A1) (Patent)
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Basic design of simple electrical circuits for controlling actuators and reading analog/digital signals
4 Oct. 2012 to 20 Jan. 2013 (3 months, 17 days)
Salesman, L’Erborista S.A.S. di Sarno Adele & C (Salerno, Italy).
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Selling products, warehouse management and cleaning
1 Nov. 2010 to 3 Mar. 2013 (2 years, 4 months, 3 days)
Web Developer, Virtual (Salerno, Italy).
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Development of dynamic websites using Java Server Page, JavaScript, ASP.NET, PHP, MySQL
Education
1 Nov. 2018 to 8 Feb. 2022
Ph.D. in Cellular and Molecular Biology (Bioinformatics), University of Rome Tor Vergata (Rome, Italy).
Supervisors: Prof. Manuela Helmer-Citterich and Dr. Ilio Vitale.
Thesis: "Investigating chromosomal instability in cancer stem cells".
Evaluation: excellent quality.
3 Oct. 2016 to 25 Oct. 2018
Master’s degree in Bioinformatics (LM-6), University of Rome Tor Vergata (Rome, Italy).
Thesis: "Energetic and functional characterization of phosphorylations involved in the co-regulation of protein interaction".
Evaluation: 110/110 cum laude; GPA: 4.00, A+.
1 Oct. 2007 to 29 Oct. 2010
Bachelor’s degree in Computer Engineering (L-8), University of Salerno (Salerno, Italy).
Thesis: "High Dynamic Range (HDR) methods for industrial inspection applications".
Evaluation: 110/110 cum laude; GPA: 4.00, A+.
Teaching
| Time | Course | Role | Links |
|---|---|---|---|
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Human Pangenome BYOD Analysis Workshop by H3ABioNet (Cape Town, South Africa) |
Organizer and instructor, created new material and analyzed new human genome assemblies |
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Computational Pangenomics, AFI - Alta Formazione Insubria (Pozzolo, Italy) |
Organizer and instructor, created new material and tutorials, held lessons, assisted the participants, configured the machines |
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Computational Pangenomics, University of Rome La Sapienza (Rome, Italy) |
Organizer and instructor, created new material and tutorials, held lessons, assisted the participants, configured the machines |
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MemPanG24 Pangenomics, University of Tennessee Health and Science Center (Memphis, USA) |
Organizer, instructor and chair, created new material and tutorials, held lessons, assisted the participants, configured the virtual machines |
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Data Structures for Bioinformatics (2 CFU/ECTS), Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy) |
Teacher, created new material, held all the lessons, assisted the students, did final exams |
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PhD Program in Genetics, Molecular and Cellular Biology, University of Pavia (Pavia, Italy) |
Teacher, introducing pangenomics and PGGB (PanGenome Graph Builder) |
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Advanced Bioinformatics: Data Mining and Data Integration for Life Science (1.5 CFU/ECTS), Master’s degree, Utrecht Bioinformatics Center (Utrecht, Netherlands) |
Teacher, introducing pangenomics and PGGB (PanGenome Graph Builder) |
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Pangenome & RefGraph Workshop by H3ABioNet (Cape Town, South Africa) |
Instructor, created new material and analyzed new human genome assemblies |
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Complex Trait Community & Rat Genome CTC-RG2023 (Memphis, USA) |
Organizer and instructor, created new material for the Pangenome workshop |
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MemPanG23 Pangenomics, University of Tennessee Health and Science Center (Memphis, USA) |
Organizer, instructor and chair, created new material and tutorials, held lessons, assisted the participants, configured the virtual machines |
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Advanced Bioinformatics: Data Mining and Data Integration for Life Science (1.5 CFU/ECTS), Master’s degree, Utrecht Bioinformatics Center (Utrecht, Netherlands) |
Teacher, introducing pangenomics and PGGB (PanGenome Graph Builder) |
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CPANG22 Computational PANGenomics, Instituto Gulbenkian de Ciência (Oeiras, Portugal) |
Instructor, created new material and tutorials, held some lessons, assisted the participants |
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Bioinformatics (6 CFU/ECTS), Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy) |
Tutor, reviewed the practical lessons, assisted the students |
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Computational Proteogenomics (2 CFU/ECTS), Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy) |
Exam assistant |
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Molecular Biology (8 CFU/ECTS), Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy) |
Exam assistant |
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Bioinformatics (6 CFU/ECTS), Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy) |
Exam assistant |
Symposia
| Time | Event | Role | Links |
|---|---|---|---|
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Organizer of the "Human genetic variability in the Pangenomic era" symposia |
Mentoring
| Time | University | Thesis | Links |
|---|---|---|---|
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Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy) |
Pangenome-based pipelines for unbiased ancient DNA analysis, |
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Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy) |
Benchmarking Analytical Pipelines for Single-Cell Long-Read Sequencing in Colon Cancer |
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PhD program in Systems Medicine, Computational Biology curricula, SEMM European School of Molecular Medicine (Italy) |
Dissecting the intracellular response to replication and mitotic stress in colorectal cancer for the design of novel effective (immuno)therapies |
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Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy) |
Machine learning to automatically detect the C. elegans bodies from microscope images and measure their growth over time |
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Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy) |
Analysis of the effect of SARS-CoV-2 mutations on the pairing between the viral genome and human miRNAs |
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Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy) |
Analysis of repeated sequences in lincRNA candidates for exon shuffling |
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Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy) |
Machine Learning methods applied to kinase-substrate interaction prediction |
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Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy) |
Natural Language Processing techniques for protein encoding applied to phosphorylation prediction |
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Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy) |
Study of normalization techniques' effects in gene expression correlation analyses |
Invitations
| Time | Place | Description | Links |
|---|---|---|---|
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Seminar on "Pangenomes everywhere" |
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Seminar on "Heterologous recombination in the human pangenome" |
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Invited speaker on "Heterologous recombination in the human pangenome" |
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Seminar on "Heterologous recombination in the human pangenome" |
Publications
*first authorship
| Journal | Title | Contribution | Links |
|---|---|---|---|
bioRxiv, Submitted |
The formation and propagation of human Robertsonian chromosomes |
Genetic, epigenetic, and pangenome analyses, figures, paper writing |
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bioRxiv, Submitted |
The Platinum Pedigree: A long-read benchmark for genetic variants |
Pangenome analysis |
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bioRxiv, Submitted |
Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context |
Testing, paper editing |
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bioRxiv, Submitted |
Epigenetic control and inheritance of rDNA arrays |
Nanopore reads analysis |
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bioRxiv, In review |
Complete sequencing of ape genomes |
Pangenome alignment/Divergence |
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bioRxiv, Submitted |
Genetic Modulation of Protein Expression in Rat Brain |
Pangenome graph building and analyses, paper editing |
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bioRxiv, In review |
Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery |
Pangenome graph building and analyses, structural variant calling, paper writing |
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bioRxiv, Submitted |
The complete diploid reference genome of RPE-1 identifies human phased epigenetic landscapes |
Support for the analyses and figures, Figure 2, paper writing |
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Genome Research, 2024 |
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing |
Human centromere analysis |
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Nature Methods, 2024 |
*Building pangenome graphs |
Software development, experiments, paper writing, documentation, testing |
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Bioinformatics, 2024 |
Cluster efficient pangenome graph construction with nf-core/pangenome |
Software development, paper editing |
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Genome Research, 2024 |
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation |
Pangenome graph building and analyses, paper method section writing |
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Nature, 2024 |
Recurrent evolution and selection shape structural diversity at the amylase locus |
Pangenome graph analsysis, genome assembly, paper writing and editing |
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arXiv, 2024 |
Rapid GPU-Based Pangenome Graph Layout |
Pangenomic support |
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Bioinformatics, 2024 |
*Pangenome graph layout by Path-Guided Stochastic Gradient Descent |
Algorithm implementation and evaluation, paper writing |
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Genome Biology, 2023 |
A super-pangenome of the North American wild grape species |
Support for pangenome graph building and read mapping against the graph |
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Nature, 2023 |
The complete sequence of a human Y chromosome |
Variants and Liftover |
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Frontiers in Genetics, 2023 |
Pangenome Graphs in Infectious Disease: A Comprehensive Genetic Variation Analysis of Neisseria Meningitidis leveraging Oxford Nanopore long reads |
Pangenomic analyses and support, paper editing |
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Nature, 2023 |
*Recombination between heterologous human acrocentric chromosomes |
Pangenomic analyses, Figures from 1 to 5, paper writing |
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Nature, 2023 |
A draft human pangenome reference |
Paper editing, pangenome graph creation and visualization, population genetic analysis |
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Bioinformatics, 2023 |
Optimal gap-affine alignment in O(s) space |
Testing, evaluation, Figure 2 |
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Bioinformatics, 2022 |
Unbiased pangenome graphs |
Parallelization of a bottleneck, bug fixings, experiments in multiple species |
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Nature, 2022 |
Semi-automated assembly of high-quality diploid human reference genomes |
Pangenome alignments, Jaccard, PCA and MHC analyses, Figure 2 |
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Nature Immunology, 2022 |
Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B |
Figure 6.a, 7.a, and 7.b, contributed for Figure 6.c, 6.e, performed RNA-seq, ATAC-seq, microarray data analysis, correlation analyses, TF-binding motif enrichment, survival analyses |
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Bioinformatics, 2022 |
*ODGI: understanding pangenome graphs |
Paper and documentation writing, figures and table, implemented several tools |
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Non-coding RNA Research, 2022 |
Evaluation of potential miRNA sponge effects of SARS genomes in human |
Genome sequences collection, filtering, deduplication, alignment, variant calling |
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Nucleic Acids Research, 2021 |
*BRIO: a web server for RNA sequence and structure motif scan |
Paper writing, figures and table, refactored and completed the webserver, datasets refinement |
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Communications Biology, 2021 |
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis |
Differential expression analyses, including batch effects exploration, GO/pathway enrichment analyses |
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Cancers, 2021 |
The Targeting of MRE11 or RAD51 Sensitizes Colorectal Cancer Stem Cells to CHK1 Inhibition |
Figure 1.A, helped in analyzing survival data |
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Cell Death & Disease, 2021 |
Inhibition of HECT E3 ligases as potential therapy for COVID-19 |
Figure 4, in silico 3D structures analysis |
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NAR Genomics & Bioinformatics, 2021 |
*Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments |
Paper writing, contributed to Figure 2, made Figure 3, 4, and 5, and fixed, refactored and completed the framework |
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Cell Death & Disease, 2021 |
Control of replication stress and mitosis in colorectal cancer stem cells through the interplay of PARP1, MRE11 and RAD51 |
Bioinformatics support |
Research experience
1 Nov. 2018 to 8 Nov. 2022
Bioinformatic analyses of multiomics data, University of Rome Tor Vergata (Rome, Italy).
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Germline and somatic variants analyses on Whole-Exome sequencing (WES) data: quality control, sample matching, rRNA contamination, read trimming and mapping, variant calling, and functional prediction
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Microsatellite instability (MSI) status on paired tumor-normal and tumor-only WES data
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Variant calling and differential expression analyses on RNA-seq data
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Neoantigen prediction and prioritization by integrating WES data and RNA-seq data
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Analysis of Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data
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Normalization and correlation analysis of transcriptomic microarray data (Affymetrix)
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Proteomic and phosphoproteomic analyses of Reverse Phase Protein microarray (RPPA) data
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RNA structural characterization and conservation research (Pietrosanto, Adinolfi, Guarracino et al., 2021)
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Web server development for RNA sequence and structure motif scan (Guarracino et al., 2021)
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Energetic and functional analyses of phosphorylations applied in silico on 3D structures of protein complexes
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Cox modeling and survival analysis on patient cohorts (from TCGA and cBioPortal platforms)
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Basic procedures on High Performance Computing (HPC) machines
5 Apr. 2020 to 21 Sept. 2022
Previous software development for pangenomics.
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Workflow development of a public sequence resource for on-the-fly analyses ( bh20-seq-resource)
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Development of a pangenome graph browser ( Pantograph)
Awards
| Time | Place | Description | Amount | Links |
|---|---|---|---|---|
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Student Travel Grant |
600 CHF (632.36 EUR) |
Talks & Posters
| Time | Conference | Title | Links |
|---|---|---|---|
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Multi-platform genome assembly of an SHR/OlaIpcv X BN-Lx/Cub F1 rat "trio" |
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HPRC 2024 Annual Meeting |
Lessons from the amylase locus |
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Formation and propagation of human Robertsonian chromosomes |
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The complete sequence of Robertsonian chromosomes |
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Aligning pangenomes with hierarchical wavefront algorithm |
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Building a Pangenome Graph for the HXB/BXH Recombinant Inbred Rat Strain Family: Enhanced Discovery of Complex Variants and Validation with Sanger Sequencing |
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Initial effort in generating a rat pangenome |
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Chromosome communities in the human pangenome |
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RNA secondary structure motifs involved in the interaction with RNA binding proteins |
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Chromosome communities in the human pangenome |
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A pangenome for the expanded BXD family of mice |
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ODGI: scalable tools for pangenome graphs |
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Control of replication stress and mitosis in cancer stem cells |
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Identification of RNA sequence and structure motifs for protein interaction |
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Identification of RNA sequence and structure motifs for protein interaction |
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Population genomics analyses on pangenome graphs |
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Graph Layout by Path-Guided Stochastic Gradient |
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Graph Layout by Path-Guided Stochastic Gradient |
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Scalable Variant Detection In Pangenome Models |
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COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource |
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Pantograph: Scalable Interactive Graph Genome Visualization |
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Semantic Variation Graphs - A Pangenome Ontology |
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Comprehensive analysis of human SARS-CoV-2 infection and host-virus interaction |
Courses
| Time | Place | Title | Links |
|---|---|---|---|
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A multidisciplinary approach to epistasis detection |
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Overcoming Challenges in Academic Writing: Tips for Writing Articles and Grant Applications |
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English language certification |
English Speaking Board (ESB) Level 1 (B2 CEFR), Pass with distinction |
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Best practices for RNA-Seq data analysis - ELIXIR-IIB |
Misc
| Time | Info | What | Links |
|---|---|---|---|
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Associate Member of the Human Pangenome Reference Consortium |
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Chair at the "Deciphering the complexity in neurodegeneration and cancer" workshop |
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Helper for the "Parallel Graph Traversal for Variation Graphs" project |
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Quote in the newspaper Le Monde: SARS-CoV-2 et Covid-19 |